NOTE: Most plots are interactive and you can use the legend to specify samples/treatment of interest. You can also download an .svg version of each figure within this report.


  Pre- and Post-Adapter Removal Read Stats


Table 1: Read summary stats
Sample Total_before R1_before R1_before_length R2_before R2_before_length GC_before Total_after R1_after R1_after_length R2_after R2_after_length GC_after Reads_discarded
test3 16000 8000 301 8000 301 0.44 15236 7618 300 7618 300 0.44 764
test1 16000 8000 301 8000 301 0.48 14954 7477 300 7477 300 0.48 1046
test5 16000 8000 301 8000 301 0.46 15194 7597 300 7597 300 0.46 806
test6 16000 8000 301 8000 301 0.46 15052 7526 300 7526 300 0.46 948
test2 16000 8000 301 8000 301 0.48 14702 7351 300 7351 300 0.48 1298
test4 16000 8000 301 8000 301 0.46 15056 7528 300 7528 300 0.46 944



Total number of reads before and after adapter removal


Forward (R1) and reverse (R2) read length before and after adapter removal




  Number of Reads Per Sample









  Rarefaction Curves






  Diversity Analyses Plots



Shannon diversity


## [1] "Shapiro Test of normality - data is normal p-value > 0.05"
## 
##  Shapiro-Wilk normality test
## 
## data:  resid(shannonaov)
## W = 0.96378, p-value = 0.8483
## 
## 
## --------------------------------------------------------------
## 
## [1] "Bartlett Test variance homogeneity - variance is homogeneous p-value > 0.05"
## 
##  Bartlett test of homogeneity of variances
## 
## data:  index by treatment
## Bartlett's K-squared = 2.3696, df = 1, p-value = 0.1237
## 
## 
## --------------------------------------------------------------
## 
## [1] "ANOVA Results"
##             Df Sum Sq Mean Sq F value Pr(>F)
## treatment    1 0.0186 0.01863    0.16  0.709
## Residuals    4 0.4645 0.11612               
## 
## --------------------------------------------------------------
## 
## [1] "Tukey HSD - Pairwise comparison - significant differences indicated by p-value < 0.05"
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
## 
## Fit: aov(formula = index ~ treatment, data = shannondata5_2)
## 
## $treatment
##                     diff       lwr       upr    p adj
## Group2-Group1 -0.1114473 -0.883944 0.6610495 0.709219
## 
## 
## --------------------------------------------------------------





Simpson diversity


## [1] "Shapiro Test of normality - data is normal p-value > 0.05"
## 
##  Shapiro-Wilk normality test
## 
## data:  resid(simpsonaov)
## W = 0.97915, p-value = 0.9473
## 
## 
## --------------------------------------------------------------
## 
## [1] "Bartlett Test variance homogeneity - variance is homogeneous p-value > 0.05"
## 
##  Bartlett test of homogeneity of variances
## 
## data:  index by treatment
## Bartlett's K-squared = 1.1591, df = 1, p-value = 0.2817
## 
## 
## --------------------------------------------------------------
## 
## [1] "ANOVA Results"
##             Df Sum Sq Mean Sq F value Pr(>F)
## treatment    1 0.0034  0.0034   0.085  0.785
## Residuals    4 0.1604  0.0401               
## 
## --------------------------------------------------------------
## 
## [1] "Tukey HSD - Pairwise comparison - significant differences indicated by p-value < 0.05"
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
## 
## Fit: aov(formula = index ~ treatment, data = simpsondata5_2)
## 
## $treatment
##                      diff        lwr       upr     p adj
## Group2-Group1 -0.04762309 -0.5015975 0.4063513 0.7853334
## 
## 
## --------------------------------------------------------------





Richness


## [1] "Shapiro Test of normality - data is normal p-value > 0.05"
## 
##  Shapiro-Wilk normality test
## 
## data:  resid(richaov)
## W = 0.88042, p-value = 0.271
## 
## 
## --------------------------------------------------------------
## 
## [1] "Bartlett Test variance homogeneity - variance is homogeneous p-value > 0.05"
## 
##  Bartlett test of homogeneity of variances
## 
## data:  index by treatment
## Bartlett's K-squared = 0.092238, df = 1, p-value = 0.7614
## 
## 
## --------------------------------------------------------------
## 
## [1] "ANOVA Results"
##             Df Sum Sq Mean Sq F value Pr(>F)
## treatment    1 0.3181  0.3181    1.48  0.291
## Residuals    4 0.8598  0.2150               
## 
## --------------------------------------------------------------
## 
## [1] "Tukey HSD - Pairwise comparison - significant differences indicated by p-value < 0.05"
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
## 
## Fit: aov(formula = index ~ treatment, data = richdata5_2)
## 
## $treatment
##                     diff       lwr       upr     p adj
## Group2-Group1 -0.4605252 -1.511576 0.5905262 0.2906586
## 
## 
## --------------------------------------------------------------






  Distance To Centroid 


## 
## Call:
## adonis(formula = bray.distance ~ data5$treatment) 
## 
## Permutation: free
## Number of permutations: 719
## 
## Terms added sequentially (first to last)
## 
##                 Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)
## data5$treatment  1   1.07522 1.07522  7.6237 0.65588    0.1
## Residuals        4   0.56415 0.14104         0.34412       
## Total            5   1.63937                 1.00000






  NMDS Plots


2D NMDS


## Run 0 stress 8.516666e-05 
## Run 1 stress 0 
## ... New best solution
## ... Procrustes: rmse 0.2292647  max resid 0.3555478 
## Run 2 stress 0.1420473 
## Run 3 stress 0 
## ... Procrustes: rmse 0.0763136  max resid 0.09339155 
## Run 4 stress 9.015944e-05 
## ... Procrustes: rmse 0.04246819  max resid 0.05812314 
## Run 5 stress 0.2269841 
## Run 6 stress 0.1420473 
## Run 7 stress 0 
## ... Procrustes: rmse 0.1570328  max resid 0.3247846 
## Run 8 stress 0 
## ... Procrustes: rmse 0.125224  max resid 0.2303329 
## Run 9 stress 7.999405e-05 
## ... Procrustes: rmse 0.2224407  max resid 0.38638 
## Run 10 stress 0.2269841 
## Run 11 stress 0.1420473 
## Run 12 stress 0 
## ... Procrustes: rmse 0.118559  max resid 0.220027 
## Run 13 stress 0.1420473 
## Run 14 stress 0 
## ... Procrustes: rmse 0.04684244  max resid 0.0688851 
## Run 15 stress 9.885943e-05 
## ... Procrustes: rmse 0.0678611  max resid 0.09331432 
## Run 16 stress 8.206816e-05 
## ... Procrustes: rmse 0.1550841  max resid 0.3075236 
## Run 17 stress 9.34972e-05 
## ... Procrustes: rmse 0.2065033  max resid 0.4214932 
## Run 18 stress 0 
## ... Procrustes: rmse 0.126147  max resid 0.1994897 
## Run 19 stress 0 
## ... Procrustes: rmse 0.1130878  max resid 0.1824697 
## Run 20 stress 0.1420473 
## Run 21 stress 0 
## ... Procrustes: rmse 0.1485547  max resid 0.2519089 
## Run 22 stress 0 
## ... Procrustes: rmse 0.1212342  max resid 0.2154881 
## Run 23 stress 0.2181459 
## Run 24 stress 8.200665e-05 
## ... Procrustes: rmse 0.2143283  max resid 0.429963 
## Run 25 stress 0.2181459 
## Run 26 stress 0 
## ... Procrustes: rmse 0.1002697  max resid 0.1923843 
## Run 27 stress 0 
## ... Procrustes: rmse 0.1041719  max resid 0.1422895 
## Run 28 stress 0.2269841 
## Run 29 stress 6.245777e-05 
## ... Procrustes: rmse 0.1383498  max resid 0.2163295 
## Run 30 stress 0.2029041 
## Run 31 stress 0 
## ... Procrustes: rmse 0.1241107  max resid 0.2182096 
## Run 32 stress 0 
## ... Procrustes: rmse 0.07906875  max resid 0.1253994 
## Run 33 stress 0 
## ... Procrustes: rmse 0.1103616  max resid 0.1687388 
## Run 34 stress 2.042108e-06 
## ... Procrustes: rmse 0.1339719  max resid 0.2333751 
## Run 35 stress 9.74567e-05 
## ... Procrustes: rmse 0.1284  max resid 0.1859043 
## Run 36 stress 0 
## ... Procrustes: rmse 0.07798043  max resid 0.1214119 
## Run 37 stress 0 
## ... Procrustes: rmse 0.1092728  max resid 0.1734401 
## Run 38 stress 4.775983e-05 
## ... Procrustes: rmse 0.2000035  max resid 0.4095928 
## Run 39 stress 3.886002e-05 
## ... Procrustes: rmse 0.1248505  max resid 0.2148006 
## Run 40 stress 0 
## ... Procrustes: rmse 0.1352201  max resid 0.2162602 
## Run 41 stress 0 
## ... Procrustes: rmse 0.1262112  max resid 0.1885194 
## Run 42 stress 5.339001e-05 
## ... Procrustes: rmse 0.2083404  max resid 0.3574877 
## Run 43 stress 0.2029041 
## Run 44 stress 0.1420473 
## Run 45 stress 0 
## ... Procrustes: rmse 0.102437  max resid 0.1498367 
## Run 46 stress 5.22987e-05 
## ... Procrustes: rmse 0.1817013  max resid 0.3806718 
## Run 47 stress 0 
## ... Procrustes: rmse 0.1315114  max resid 0.1869779 
## Run 48 stress 0 
## ... Procrustes: rmse 0.1296647  max resid 0.1929563 
## Run 49 stress 0 
## ... Procrustes: rmse 0.1016486  max resid 0.1490199 
## Run 50 stress 0.2181459 
## Run 51 stress 0 
## ... Procrustes: rmse 0.1666925  max resid 0.2812047 
## Run 52 stress 0 
## ... Procrustes: rmse 0.04865803  max resid 0.07450743 
## Run 53 stress 0.2181459 
## Run 54 stress 0 
## ... Procrustes: rmse 0.1072679  max resid 0.1833416 
## Run 55 stress 9.402591e-05 
## ... Procrustes: rmse 0.1652184  max resid 0.2871537 
## Run 56 stress 0 
## ... Procrustes: rmse 0.2055956  max resid 0.3592358 
## Run 57 stress 0 
## ... Procrustes: rmse 0.09122371  max resid 0.1355847 
## Run 58 stress 0.2181459 
## Run 59 stress 0 
## ... Procrustes: rmse 0.07966123  max resid 0.1270126 
## Run 60 stress 0.2269841 
## Run 61 stress 0 
## ... Procrustes: rmse 0.06335752  max resid 0.09949353 
## Run 62 stress 0 
## ... Procrustes: rmse 0.1554245  max resid 0.2581932 
## Run 63 stress 0.2181459 
## Run 64 stress 0.2029041 
## Run 65 stress 0 
## ... Procrustes: rmse 0.1185207  max resid 0.1752303 
## Run 66 stress 4.042124e-05 
## ... Procrustes: rmse 0.2143988  max resid 0.432039 
## Run 67 stress 0 
## ... Procrustes: rmse 0.08432112  max resid 0.131646 
## Run 68 stress 0.2181459 
## Run 69 stress 9.688414e-05 
## ... Procrustes: rmse 0.1926112  max resid 0.3977367 
## Run 70 stress 8.291099e-05 
## ... Procrustes: rmse 0.2189258  max resid 0.3867534 
## Run 71 stress 9.960685e-05 
## ... Procrustes: rmse 0.2237682  max resid 0.4312248 
## Run 72 stress 3.088143e-05 
## ... Procrustes: rmse 0.07400363  max resid 0.1026921 
## Run 73 stress 0.2269841 
## Run 74 stress 0.2181459 
## Run 75 stress 0.1420473 
## Run 76 stress 0 
## ... Procrustes: rmse 0.0777429  max resid 0.1083593 
## Run 77 stress 0.1420473 
## Run 78 stress 0 
## ... Procrustes: rmse 0.09935545  max resid 0.1493743 
## Run 79 stress 0.2181459 
## Run 80 stress 0 
## ... Procrustes: rmse 0.08612822  max resid 0.1408433 
## Run 81 stress 9.791028e-05 
## ... Procrustes: rmse 0.2055398  max resid 0.4106227 
## Run 82 stress 0.1420473 
## Run 83 stress 0.2181459 
## Run 84 stress 0 
## ... Procrustes: rmse 0.08166741  max resid 0.1198376 
## Run 85 stress 0 
## ... Procrustes: rmse 0.1021789  max resid 0.1732992 
## Run 86 stress 0 
## ... Procrustes: rmse 0.09787576  max resid 0.1472266 
## Run 87 stress 0 
## ... Procrustes: rmse 0.113549  max resid 0.1834908 
## Run 88 stress 9.772695e-05 
## ... Procrustes: rmse 0.2057312  max resid 0.3518287 
## Run 89 stress 0 
## ... Procrustes: rmse 0.1328987  max resid 0.2023825 
## Run 90 stress 0.2159914 
## Run 91 stress 0 
## ... Procrustes: rmse 0.08548373  max resid 0.1061624 
## *** No convergence -- monoMDS stopping criteria:
##     63: stress < smin
##     11: stress ratio > sratmax
##     17: scale factor of the gradient < sfgrmin
## [1] "No Convergence"





3D NMDS


## Run 0 stress 3.864101e-05 
## Run 1 stress 9.618523e-05 
## ... Procrustes: rmse 0.08265051  max resid 0.09880757 
## Run 2 stress 9.674701e-05 
## ... Procrustes: rmse 0.09964885  max resid 0.122559 
## Run 3 stress 6.775705e-06 
## ... New best solution
## ... Procrustes: rmse 0.169141  max resid 0.2281253 
## Run 4 stress 0 
## ... New best solution
## ... Procrustes: rmse 0.1467183  max resid 0.2523122 
## Run 5 stress 6.833422e-05 
## ... Procrustes: rmse 0.1648122  max resid 0.2214621 
## Run 6 stress 0 
## ... Procrustes: rmse 0.2357521  max resid 0.3990029 
## Run 7 stress 0 
## ... Procrustes: rmse 0.1903864  max resid 0.2834956 
## Run 8 stress 6.002245e-05 
## ... Procrustes: rmse 0.1519616  max resid 0.2161842 
## Run 9 stress 9.487699e-05 
## ... Procrustes: rmse 0.1590915  max resid 0.2205284 
## Run 10 stress 9.662979e-05 
## ... Procrustes: rmse 0.1765616  max resid 0.2739234 
## Run 11 stress 0 
## ... Procrustes: rmse 0.1796174  max resid 0.2625688 
## Run 12 stress 0 
## ... Procrustes: rmse 0.07320751  max resid 0.1208306 
## Run 13 stress 0 
## ... Procrustes: rmse 0.0726035  max resid 0.104632 
## Run 14 stress 0 
## ... Procrustes: rmse 0.1537718  max resid 0.2466778 
## Run 15 stress 0 
## ... Procrustes: rmse 0.1827372  max resid 0.2756763 
## Run 16 stress 8.77228e-05 
## ... Procrustes: rmse 0.1231251  max resid 0.2167976 
## Run 17 stress 9.589444e-05 
## ... Procrustes: rmse 0.177905  max resid 0.2551409 
## Run 18 stress 0 
## ... Procrustes: rmse 0.2317487  max resid 0.3978466 
## Run 19 stress 9.754167e-05 
## ... Procrustes: rmse 0.2134792  max resid 0.352959 
## Run 20 stress 0 
## ... Procrustes: rmse 0.1380613  max resid 0.2526259 
## Run 21 stress 0 
## ... Procrustes: rmse 0.2264863  max resid 0.4021794 
## Run 22 stress 0 
## ... Procrustes: rmse 0.08355771  max resid 0.1584266 
## Run 23 stress 0 
## ... Procrustes: rmse 0.1980071  max resid 0.2980975 
## Run 24 stress 4.892489e-05 
## ... Procrustes: rmse 0.2425368  max resid 0.4394601 
## Run 25 stress 0 
## ... Procrustes: rmse 0.1088582  max resid 0.183734 
## Run 26 stress 0 
## ... Procrustes: rmse 0.1762248  max resid 0.2120584 
## Run 27 stress 0 
## ... Procrustes: rmse 0.2065393  max resid 0.3882593 
## Run 28 stress 0.1512494 
## Run 29 stress 8.913664e-05 
## ... Procrustes: rmse 0.157248  max resid 0.2302327 
## Run 30 stress 9.861122e-05 
## ... Procrustes: rmse 0.1827239  max resid 0.2727363 
## Run 31 stress 5.403868e-05 
## ... Procrustes: rmse 0.2284711  max resid 0.3857031 
## Run 32 stress 0 
## ... Procrustes: rmse 0.08806296  max resid 0.1562183 
## Run 33 stress 0 
## ... Procrustes: rmse 0.2039279  max resid 0.2769838 
## Run 34 stress 9.690529e-05 
## ... Procrustes: rmse 0.1640622  max resid 0.2358574 
## Run 35 stress 1.601223e-05 
## ... Procrustes: rmse 0.1083471  max resid 0.1393038 
## Run 36 stress 9.75765e-05 
## ... Procrustes: rmse 0.1679021  max resid 0.2425338 
## Run 37 stress 0 
## ... Procrustes: rmse 0.1317383  max resid 0.223774 
## Run 38 stress 0 
## ... Procrustes: rmse 0.1073714  max resid 0.1490398 
## Run 39 stress 9.540333e-05 
## ... Procrustes: rmse 0.1226659  max resid 0.2115139 
## Run 40 stress 8.011839e-05 
## ... Procrustes: rmse 0.08216674  max resid 0.1055457 
## Run 41 stress 0 
## ... Procrustes: rmse 0.1466075  max resid 0.2236215 
## Run 42 stress 9.880402e-05 
## ... Procrustes: rmse 0.167597  max resid 0.2446863 
## Run 43 stress 5.03596e-05 
## ... Procrustes: rmse 0.226756  max resid 0.2709706 
## Run 44 stress 0 
## ... Procrustes: rmse 0.1308585  max resid 0.1865175 
## Run 45 stress 0 
## ... Procrustes: rmse 0.2285948  max resid 0.4096774 
## Run 46 stress 0 
## ... Procrustes: rmse 0.2375731  max resid 0.3947861 
## Run 47 stress 8.016021e-05 
## ... Procrustes: rmse 0.2294485  max resid 0.4029602 
## Run 48 stress 9.958433e-05 
## ... Procrustes: rmse 0.1623946  max resid 0.265649 
## Run 49 stress 0 
## ... Procrustes: rmse 0.07481238  max resid 0.11158 
## Run 50 stress 4.471901e-05 
## ... Procrustes: rmse 0.03892019  max resid 0.05417969 
## Run 51 stress 8.715565e-05 
## ... Procrustes: rmse 0.2300562  max resid 0.30818 
## Run 52 stress 0 
## ... Procrustes: rmse 0.08511088  max resid 0.151068 
## Run 53 stress 0 
## ... Procrustes: rmse 0.2180165  max resid 0.3636724 
## Run 54 stress 0 
## ... Procrustes: rmse 0.1763519  max resid 0.2955852 
## Run 55 stress 6.789788e-05 
## ... Procrustes: rmse 0.1361742  max resid 0.1800913 
## Run 56 stress 0 
## ... Procrustes: rmse 0.1431829  max resid 0.2190628 
## Run 57 stress 0 
## ... Procrustes: rmse 0.1594864  max resid 0.2155361 
## Run 58 stress 0 
## ... Procrustes: rmse 0.2005132  max resid 0.3524586 
## Run 59 stress 0 
## ... Procrustes: rmse 0.165439  max resid 0.1974747 
## Run 60 stress 0 
## ... Procrustes: rmse 0.09497237  max resid 0.1525758 
## Run 61 stress 9.280306e-05 
## ... Procrustes: rmse 0.2259055  max resid 0.4013282 
## Run 62 stress 2.43618e-05 
## ... Procrustes: rmse 0.09564025  max resid 0.1234208 
## Run 63 stress 9.240547e-05 
## ... Procrustes: rmse 0.1723737  max resid 0.308795 
## Run 64 stress 0 
## ... Procrustes: rmse 0.07759072  max resid 0.1100485 
## Run 65 stress 0 
## ... Procrustes: rmse 0.2008711  max resid 0.3765499 
## Run 66 stress 0 
## ... Procrustes: rmse 0.1895162  max resid 0.3271299 
## Run 67 stress 0 
## ... Procrustes: rmse 0.1957091  max resid 0.3944642 
## Run 68 stress 8.97237e-05 
## ... Procrustes: rmse 0.134721  max resid 0.2008305 
## Run 69 stress 0 
## ... Procrustes: rmse 0.1405048  max resid 0.2502531 
## Run 70 stress 0 
## ... Procrustes: rmse 0.2011602  max resid 0.2823315 
## Run 71 stress 5.166469e-05 
## ... Procrustes: rmse 0.08041961  max resid 0.1221728 
## Run 72 stress 0 
## ... Procrustes: rmse 0.2087462  max resid 0.3323884 
## Run 73 stress 0 
## ... Procrustes: rmse 0.1605193  max resid 0.2681912 
## Run 74 stress 9.533563e-05 
## ... Procrustes: rmse 0.1845128  max resid 0.2922687 
## Run 75 stress 7.458746e-05 
## ... Procrustes: rmse 0.1716324  max resid 0.2315354 
## Run 76 stress 0.1512494 
## Run 77 stress 9.886174e-05 
## ... Procrustes: rmse 0.1384755  max resid 0.2417798 
## Run 78 stress 0 
## ... Procrustes: rmse 0.1214548  max resid 0.1679333 
## Run 79 stress 0.1512494 
## Run 80 stress 6.811102e-05 
## ... Procrustes: rmse 0.1422093  max resid 0.2429922 
## Run 81 stress 8.087179e-05 
## ... Procrustes: rmse 0.1542973  max resid 0.2198985 
## Run 82 stress 8.625092e-05 
## ... Procrustes: rmse 0.2434134  max resid 0.440316 
## Run 83 stress 0 
## ... Procrustes: rmse 0.2358538  max resid 0.4260843 
## Run 84 stress 7.314124e-05 
## ... Procrustes: rmse 0.1208427  max resid 0.1643601 
## Run 85 stress 9.443833e-05 
## ... Procrustes: rmse 0.2304085  max resid 0.4253988 
## Run 86 stress 3.64926e-05 
## ... Procrustes: rmse 0.1465787  max resid 0.2140089 
## Run 87 stress 0 
## ... Procrustes: rmse 0.09510719  max resid 0.1248787 
## Run 88 stress 0 
## ... Procrustes: rmse 0.237263  max resid 0.3521101 
## Run 89 stress 9.093125e-05 
## ... Procrustes: rmse 0.1254003  max resid 0.1743458 
## Run 90 stress 0 
## ... Procrustes: rmse 0.1769971  max resid 0.3197116 
## Run 91 stress 0 
## ... Procrustes: rmse 0.04310136  max resid 0.06127615 
## *** No convergence -- monoMDS stopping criteria:
##     88: stress < smin
##      2: stress ratio > sratmax
##      1: scale factor of the gradient < sfgrmin
## [1] "No Convergence"






  Relative Abundance Per Sample






  Sequence Abundance Per Treatment






  Pairwise Percent Similarity Heatmap








  Taxonomy Results Visualization








  Phylogenetic Tree



This tree is a maximum likelihood tree made with IQTREE2 and the parameters you specified in the vampirus.config file. Also, this is an interactive tree, you can zoom in and hover on nodes to know the sequence ID. For a better visualization of this tree, you can find the *.treefile with bootstrap support values within the results directory and visualize using programs like FigTree or ITOL. If you ran the MED analysis, the colors of the nodes correspond to the MED group they were assigned to.






Post Minimum Entropy Decomposition (MED) Analyses

  MED Group Breakdown Table



Table: Aminotype MED Table
Group1 Group2 Group3 Group4 Group5
vAMPtest_AminoType1 vAMPtest_AminoType10 vAMPtest_AminoType7 vAMPtest_AminoType16 vAMPtest_AminoType11
vAMPtest_AminoType13 vAMPtest_AminoType12 vAMPtest_AminoType8 vAMPtest_AminoType3
vAMPtest_AminoType14 vAMPtest_AminoType15
vAMPtest_AminoType2 vAMPtest_AminoType4
vAMPtest_AminoType5 vAMPtest_AminoType9
vAMPtest_AminoType6






  Post-MED Relative Abundance Plot








  Post-Med Rarefaction Curves









  Post-MED Diversity Analyses Plots



Post-MED Shannon diversity


## [1] "Shapiro Test of normality - data is normal p-value > 0.05"
## 
##  Shapiro-Wilk normality test
## 
## data:  resid(shannonaov)
## W = 0.92677, p-value = 0.5554
## 
## 
## --------------------------------------------------------------
## 
## [1] "Bartlett Test variance homogeneity - variance is homogeneous p-value > 0.05"
## 
##  Bartlett test of homogeneity of variances
## 
## data:  index by treatment
## Bartlett's K-squared = 2.0493, df = 1, p-value = 0.1523
## 
## 
## --------------------------------------------------------------
## 
## [1] "ANOVA Results"
##             Df  Sum Sq Mean Sq F value Pr(>F)
## treatment    1 0.00181 0.00181   0.043  0.846
## Residuals    4 0.16991 0.04248               
## 
## --------------------------------------------------------------
## 
## [1] "Tukey HSD - Pairwise comparison - significant differences indicated by p-value < 0.05"
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
## 
## Fit: aov(formula = index ~ treatment, data = shannondata5_2)
## 
## $treatment
##                      diff        lwr       upr     p adj
## Group2-Group1 -0.03477559 -0.5019946 0.4324434 0.8463728
## 
## 
## --------------------------------------------------------------





Post-MED Simpson diversity


## [1] "Shapiro Test of normality - data is normal p-value > 0.05"
## 
##  Shapiro-Wilk normality test
## 
## data:  resid(simpsonaov)
## W = 0.90983, p-value = 0.4353
## 
## 
## --------------------------------------------------------------
## 
## [1] "Bartlett Test variance homogeneity - variance is homogeneous p-value > 0.05"
## 
##  Bartlett test of homogeneity of variances
## 
## data:  index by treatment
## Bartlett's K-squared = 2.52, df = 1, p-value = 0.1124
## 
## 
## --------------------------------------------------------------
## 
## [1] "ANOVA Results"
##             Df  Sum Sq  Mean Sq F value Pr(>F)
## treatment    1 0.00204 0.002037   0.111  0.756
## Residuals    4 0.07336 0.018339               
## 
## --------------------------------------------------------------
## 
## [1] "Tukey HSD - Pairwise comparison - significant differences indicated by p-value < 0.05"
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
## 
## Fit: aov(formula = index ~ treatment, data = simpsondata5_2)
## 
## $treatment
##                      diff        lwr       upr     p adj
## Group2-Group1 -0.03685422 -0.3438498 0.2701413 0.7556408
## 
## 
## --------------------------------------------------------------





Post-MED Richness


## [1] "Shapiro Test of normality - data is normal if p-value > 0.05"
## 
##  Shapiro-Wilk normality test
## 
## data:  resid(richaov)
## W = 0.83508, p-value = 0.1186
## 
## 
## --------------------------------------------------------------
## 
## [1] "Bartlett Test variance homogeneity - variance is homogeneous if p-value > 0.05"
## 
##  Bartlett test of homogeneity of variances
## 
## data:  index by treatment
## Bartlett's K-squared = 21.019, df = 1, p-value = 4.547e-06
## 
## 
## --------------------------------------------------------------
## 
## [1] "Data either not normal or variance not homogenous"
## [1] "Kruskal-Wallis Test - test significant if p <.05"
## 
##  Kruskal-Wallis rank sum test
## 
## data:  index by treatment
## Kruskal-Wallis chi-squared = 0.42857, df = 1, p-value = 0.5127
## 
## 
## --------------------------------------------------------------
## 
## [1] "Data not significant. Skipping pairwise comparison"
## 
## --------------------------------------------------------------
## 
## [1] "ANOVA - one or more of the assumptions not met, take with a grain of salt."
##             Df Sum Sq Mean Sq F value Pr(>F)
## treatment    1 0.5141  0.5141   2.342  0.201
## Residuals    4 0.8778  0.2195               
## 
## --------------------------------------------------------------






  Post-MED Distance To Centroid 


## 
## Call:
## adonis(formula = bray.distance ~ meddata5$treatment) 
## 
## Permutation: free
## Number of permutations: 719
## 
## Terms added sequentially (first to last)
## 
##                    Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)
## meddata5$treatment  1   0.72083 0.72083  13.455 0.77084    0.1
## Residuals           4   0.21430 0.05357         0.22916       
## Total               5   0.93513                 1.00000






  NMDS Plots


Post-MED 2D NMDS


## Run 0 stress 0 
## Run 1 stress 9.585412e-05 
## ... Procrustes: rmse 0.07327924  max resid 0.1089457 
## Run 2 stress 9.857982e-05 
## ... Procrustes: rmse 0.1270674  max resid 0.2463404 
## Run 3 stress 9.861741e-05 
## ... Procrustes: rmse 0.1502306  max resid 0.2849561 
## Run 4 stress 0 
## ... Procrustes: rmse 0.1801679  max resid 0.3507864 
## Run 5 stress 9.751848e-05 
## ... Procrustes: rmse 0.07208713  max resid 0.1296016 
## Run 6 stress 0 
## ... Procrustes: rmse 0.05254968  max resid 0.1146751 
## Run 7 stress 9.328431e-05 
## ... Procrustes: rmse 0.07734704  max resid 0.1424702 
## Run 8 stress 0.2475416 
## Run 9 stress 0 
## ... Procrustes: rmse 0.1868644  max resid 0.3632897 
## Run 10 stress 8.874472e-05 
## ... Procrustes: rmse 0.07841869  max resid 0.1244634 
## Run 11 stress 9.802216e-05 
## ... Procrustes: rmse 0.1582175  max resid 0.2170241 
## Run 12 stress 0 
## ... Procrustes: rmse 0.09463104  max resid 0.1394922 
## Run 13 stress 9.999985e-05 
## ... Procrustes: rmse 0.1485101  max resid 0.2708957 
## Run 14 stress 9.712869e-05 
## ... Procrustes: rmse 0.1243946  max resid 0.2448997 
## Run 15 stress 9.426449e-05 
## ... Procrustes: rmse 0.1405494  max resid 0.2029695 
## Run 16 stress 7.305698e-05 
## ... Procrustes: rmse 0.08175434  max resid 0.1129446 
## Run 17 stress 9.946186e-05 
## ... Procrustes: rmse 0.06873862  max resid 0.1051037 
## Run 18 stress 7.610085e-05 
## ... Procrustes: rmse 0.1413648  max resid 0.2653288 
## Run 19 stress 9.858073e-05 
## ... Procrustes: rmse 0.1755062  max resid 0.3409782 
## Run 20 stress 9.456826e-05 
## ... Procrustes: rmse 0.1347099  max resid 0.2386779 
## Run 21 stress 9.183441e-05 
## ... Procrustes: rmse 0.1258241  max resid 0.2476287 
## Run 22 stress 0 
## ... Procrustes: rmse 0.1532964  max resid 0.3114371 
## Run 23 stress 5.756077e-05 
## ... Procrustes: rmse 0.07489994  max resid 0.1093775 
## Run 24 stress 0 
## ... Procrustes: rmse 0.1401128  max resid 0.2620271 
## Run 25 stress 9.887306e-05 
## ... Procrustes: rmse 0.03401171  max resid 0.04746078 
## Run 26 stress 7.080787e-05 
## ... Procrustes: rmse 0.08441362  max resid 0.1380451 
## Run 27 stress 4.617498e-05 
## ... Procrustes: rmse 0.0960515  max resid 0.1432842 
## Run 28 stress 0.2181459 
## Run 29 stress 0.1420473 
## Run 30 stress 9.910669e-05 
## ... Procrustes: rmse 0.1468215  max resid 0.2834265 
## Run 31 stress 0.2181459 
## Run 32 stress 1.686234e-05 
## ... Procrustes: rmse 0.09406121  max resid 0.1953348 
## Run 33 stress 6.999688e-06 
## ... Procrustes: rmse 0.1514338  max resid 0.2838615 
## Run 34 stress 9.989874e-05 
## ... Procrustes: rmse 0.1043052  max resid 0.1800418 
## Run 35 stress 0.2181459 
## Run 36 stress 7.031922e-05 
## ... Procrustes: rmse 0.1358158  max resid 0.2834797 
## Run 37 stress 9.93899e-05 
## ... Procrustes: rmse 0.1350616  max resid 0.2565868 
## Run 38 stress 8.927707e-05 
## ... Procrustes: rmse 0.1458258  max resid 0.2069644 
## Run 39 stress 8.952397e-05 
## ... Procrustes: rmse 0.1362748  max resid 0.2540981 
## Run 40 stress 0.2181459 
## Run 41 stress 0.2181459 
## Run 42 stress 9.759003e-05 
## ... Procrustes: rmse 0.1634158  max resid 0.2746343 
## Run 43 stress 0.2181459 
## Run 44 stress 0.2181459 
## Run 45 stress 9.87518e-05 
## ... Procrustes: rmse 0.1457379  max resid 0.2066602 
## Run 46 stress 9.046244e-05 
## ... Procrustes: rmse 0.1337007  max resid 0.25568 
## Run 47 stress 9.998735e-05 
## ... Procrustes: rmse 0.04981747  max resid 0.07810493 
## Run 48 stress 9.980543e-05 
## ... Procrustes: rmse 0.1272336  max resid 0.2487549 
## Run 49 stress 0.2181459 
## Run 50 stress 0.2673072 
## Run 51 stress 9.993578e-05 
## ... Procrustes: rmse 0.09695027  max resid 0.1444623 
## Run 52 stress 0.2673072 
## Run 53 stress 0.000134598 
## ... Procrustes: rmse 0.1101945  max resid 0.1854303 
## Run 54 stress 9.907934e-05 
## ... Procrustes: rmse 0.1497929  max resid 0.2751593 
## Run 55 stress 9.946331e-05 
## ... Procrustes: rmse 0.08546929  max resid 0.1464614 
## Run 56 stress 6.777974e-05 
## ... Procrustes: rmse 0.07446326  max resid 0.1086965 
## Run 57 stress 9.996264e-05 
## ... Procrustes: rmse 0.09074312  max resid 0.1343754 
## Run 58 stress 0.2181459 
## Run 59 stress 9.719748e-05 
## ... Procrustes: rmse 0.1128387  max resid 0.2188887 
## Run 60 stress 1.065671e-05 
## ... Procrustes: rmse 0.1099643  max resid 0.221548 
## Run 61 stress 5.878816e-05 
## ... Procrustes: rmse 0.1446279  max resid 0.2607854 
## Run 62 stress 0 
## ... Procrustes: rmse 0.1256665  max resid 0.2642728 
## Run 63 stress 9.918995e-05 
## ... Procrustes: rmse 0.1403145  max resid 0.2776022 
## Run 64 stress 9.7122e-05 
## ... Procrustes: rmse 0.1434446  max resid 0.2727137 
## Run 65 stress 9.157868e-05 
## ... Procrustes: rmse 0.1097596  max resid 0.179497 
## Run 66 stress 9.93306e-05 
## ... Procrustes: rmse 0.1234979  max resid 0.1758401 
## Run 67 stress 8.919613e-05 
## ... Procrustes: rmse 0.128694  max resid 0.2334423 
## Run 68 stress 9.985828e-05 
## ... Procrustes: rmse 0.1466615  max resid 0.2288707 
## Run 69 stress 0.2673072 
## Run 70 stress 2.793785e-05 
## ... Procrustes: rmse 0.1506661  max resid 0.2819387 
## Run 71 stress 7.619131e-05 
## ... Procrustes: rmse 0.1444494  max resid 0.276718 
## Run 72 stress 0.2673072 
## Run 73 stress 7.984382e-05 
## ... Procrustes: rmse 0.1552394  max resid 0.2859154 
## Run 74 stress 0 
## ... Procrustes: rmse 0.1140415  max resid 0.2347693 
## Run 75 stress 7.725195e-05 
## ... Procrustes: rmse 0.1857908  max resid 0.3160335 
## Run 76 stress 9.95308e-05 
## ... Procrustes: rmse 0.08300283  max resid 0.1577888 
## Run 77 stress 8.805808e-05 
## ... Procrustes: rmse 0.1346856  max resid 0.238693 
## Run 78 stress 0.2269841 
## Run 79 stress 9.647378e-05 
## ... Procrustes: rmse 0.1434534  max resid 0.2054263 
## Run 80 stress 0 
## ... Procrustes: rmse 0.1227926  max resid 0.2340298 
## Run 81 stress 9.995321e-05 
## ... Procrustes: rmse 0.200892  max resid 0.3686475 
## Run 82 stress 9.978573e-05 
## ... Procrustes: rmse 0.1080433  max resid 0.199099 
## Run 83 stress 9.893066e-05 
## ... Procrustes: rmse 0.1641548  max resid 0.3152901 
## Run 84 stress 9.825552e-05 
## ... Procrustes: rmse 0.1333982  max resid 0.1959094 
## Run 85 stress 9.997688e-05 
## ... Procrustes: rmse 0.1389627  max resid 0.2597169 
## Run 86 stress 9.331601e-05 
## ... Procrustes: rmse 0.1560821  max resid 0.215252 
## Run 87 stress 9.928466e-05 
## ... Procrustes: rmse 0.1461129  max resid 0.207274 
## Run 88 stress 0 
## ... Procrustes: rmse 0.08178748  max resid 0.1136605 
## Run 89 stress 9.776469e-05 
## ... Procrustes: rmse 0.1284732  max resid 0.2447713 
## Run 90 stress 0.1420473 
## Run 91 stress 9.999834e-05 
## ... Procrustes: rmse 0.1713422  max resid 0.3100415 
## *** No convergence -- monoMDS stopping criteria:
##      1: no. of iterations >= maxit
##     73: stress < smin
##      5: stress ratio > sratmax
##     12: scale factor of the gradient < sfgrmin
## [1] "No Convergence"





Post-MED 3D NMDS


## Run 0 stress 0 
## Run 1 stress 9.746115e-05 
## ... Procrustes: rmse 0.1794925  max resid 0.2554082 
## Run 2 stress 9.726057e-05 
## ... Procrustes: rmse 0.09336036  max resid 0.112527 
## Run 3 stress 0 
## ... Procrustes: rmse 0.1845616  max resid 0.261067 
## Run 4 stress 9.811586e-05 
## ... Procrustes: rmse 0.1654116  max resid 0.2377823 
## Run 5 stress 9.897519e-05 
## ... Procrustes: rmse 0.1636414  max resid 0.315313 
## Run 6 stress 9.905148e-05 
## ... Procrustes: rmse 0.1247494  max resid 0.143512 
## Run 7 stress 9.038443e-05 
## ... Procrustes: rmse 0.2412218  max resid 0.3562837 
## Run 8 stress 0 
## ... Procrustes: rmse 0.2392688  max resid 0.356421 
## Run 9 stress 9.740945e-05 
## ... Procrustes: rmse 0.1264608  max resid 0.1927137 
## Run 10 stress 9.656648e-05 
## ... Procrustes: rmse 0.2238776  max resid 0.3423013 
## Run 11 stress 0 
## ... Procrustes: rmse 0.2068343  max resid 0.291535 
## Run 12 stress 1.887865e-06 
## ... Procrustes: rmse 0.2289719  max resid 0.3418164 
## Run 13 stress 0 
## ... Procrustes: rmse 0.1833294  max resid 0.290401 
## Run 14 stress 0 
## ... Procrustes: rmse 0.2369303  max resid 0.3563845 
## Run 15 stress 9.109824e-05 
## ... Procrustes: rmse 0.1728675  max resid 0.3197143 
## Run 16 stress 0 
## ... Procrustes: rmse 0.2229369  max resid 0.3374696 
## Run 17 stress 8.290753e-05 
## ... Procrustes: rmse 0.1246337  max resid 0.1510449 
## Run 18 stress 9.944355e-05 
## ... Procrustes: rmse 0.1973032  max resid 0.3080051 
## Run 19 stress 8.083138e-05 
## ... Procrustes: rmse 0.2290339  max resid 0.3520068 
## Run 20 stress 6.792144e-05 
## ... Procrustes: rmse 0.1674355  max resid 0.2190931 
## Run 21 stress 9.528436e-05 
## ... Procrustes: rmse 0.2055821  max resid 0.2979368 
## Run 22 stress 8.075265e-05 
## ... Procrustes: rmse 0.2223715  max resid 0.2711622 
## Run 23 stress 0 
## ... Procrustes: rmse 0.1817135  max resid 0.2571223 
## Run 24 stress 9.6965e-05 
## ... Procrustes: rmse 0.2245289  max resid 0.3488218 
## Run 25 stress 9.603039e-05 
## ... Procrustes: rmse 0.2555124  max resid 0.3696133 
## Run 26 stress 9.923892e-05 
## ... Procrustes: rmse 0.1156229  max resid 0.1503739 
## Run 27 stress 8.609133e-05 
## ... Procrustes: rmse 0.139489  max resid 0.2338511 
## Run 28 stress 8.894788e-05 
## ... Procrustes: rmse 0.1910622  max resid 0.3252138 
## Run 29 stress 4.585002e-05 
## ... Procrustes: rmse 0.2515775  max resid 0.34437 
## Run 30 stress 8.491532e-05 
## ... Procrustes: rmse 0.1831631  max resid 0.2346807 
## Run 31 stress 9.974779e-05 
## ... Procrustes: rmse 0.1204997  max resid 0.2189615 
## Run 32 stress 9.691362e-05 
## ... Procrustes: rmse 0.229504  max resid 0.3500407 
## Run 33 stress 6.385353e-05 
## ... Procrustes: rmse 0.2333178  max resid 0.3463476 
## Run 34 stress 6.783829e-05 
## ... Procrustes: rmse 0.1463079  max resid 0.1961894 
## Run 35 stress 0 
## ... Procrustes: rmse 0.1475202  max resid 0.2459833 
## Run 36 stress 0 
## ... Procrustes: rmse 0.1865431  max resid 0.2479839 
## Run 37 stress 9.483871e-05 
## ... Procrustes: rmse 0.1761117  max resid 0.3146322 
## Run 38 stress 2.104829e-06 
## ... Procrustes: rmse 0.1867573  max resid 0.3334097 
## Run 39 stress 9.997529e-05 
## ... Procrustes: rmse 0.2149516  max resid 0.3321053 
## Run 40 stress 5.295879e-05 
## ... Procrustes: rmse 0.2167892  max resid 0.3151854 
## Run 41 stress 9.646146e-05 
## ... Procrustes: rmse 0.2137914  max resid 0.3633107 
## Run 42 stress 6.275657e-05 
## ... Procrustes: rmse 0.1199679  max resid 0.160565 
## Run 43 stress 9.545984e-05 
## ... Procrustes: rmse 0.04180981  max resid 0.07187198 
## Run 44 stress 7.542458e-05 
## ... Procrustes: rmse 0.1997764  max resid 0.2482091 
## Run 45 stress 9.905097e-05 
## ... Procrustes: rmse 0.1352612  max resid 0.2146732 
## Run 46 stress 9.667386e-05 
## ... Procrustes: rmse 0.2231514  max resid 0.3419346 
## Run 47 stress 0 
## ... Procrustes: rmse 0.1945145  max resid 0.271751 
## Run 48 stress 9.950043e-05 
## ... Procrustes: rmse 0.1863854  max resid 0.3237835 
## Run 49 stress 9.801513e-05 
## ... Procrustes: rmse 0.2416272  max resid 0.3665619 
## Run 50 stress 7.348622e-05 
## ... Procrustes: rmse 0.2576533  max resid 0.3622165 
## Run 51 stress 9.871815e-05 
## ... Procrustes: rmse 0.1711456  max resid 0.2931756 
## Run 52 stress 0 
## ... Procrustes: rmse 0.1568618  max resid 0.2144868 
## Run 53 stress 6.171768e-05 
## ... Procrustes: rmse 0.2467415  max resid 0.3323091 
## Run 54 stress 9.02198e-05 
## ... Procrustes: rmse 0.1655323  max resid 0.270452 
## Run 55 stress 9.717595e-05 
## ... Procrustes: rmse 0.188402  max resid 0.3248317 
## Run 56 stress 9.970836e-05 
## ... Procrustes: rmse 0.2418892  max resid 0.3688925 
## Run 57 stress 8.883428e-05 
## ... Procrustes: rmse 0.2431958  max resid 0.3358697 
## Run 58 stress 8.450146e-05 
## ... Procrustes: rmse 0.2307265  max resid 0.3272124 
## Run 59 stress 0 
## ... Procrustes: rmse 0.1779714  max resid 0.2597214 
## Run 60 stress 0 
## ... Procrustes: rmse 0.1472528  max resid 0.2282055 
## Run 61 stress 0.1275225 
## Run 62 stress 8.067923e-05 
## ... Procrustes: rmse 0.2379497  max resid 0.3672265 
## Run 63 stress 2.710865e-05 
## ... Procrustes: rmse 0.2462116  max resid 0.3859162 
## Run 64 stress 4.979447e-05 
## ... Procrustes: rmse 0.2134418  max resid 0.3177205 
## Run 65 stress 9.378711e-05 
## ... Procrustes: rmse 0.1764649  max resid 0.3293835 
## Run 66 stress 8.716384e-05 
## ... Procrustes: rmse 0.1996285  max resid 0.2811454 
## Run 67 stress 9.06816e-05 
## ... Procrustes: rmse 0.2476572  max resid 0.3705361 
## Run 68 stress 7.708894e-05 
## ... Procrustes: rmse 0.1088011  max resid 0.2109173 
## Run 69 stress 8.380303e-05 
## ... Procrustes: rmse 0.1984961  max resid 0.2781993 
## Run 70 stress 0.1512494 
## Run 71 stress 9.203062e-05 
## ... Procrustes: rmse 0.1605292  max resid 0.2669709 
## Run 72 stress 7.079012e-05 
## ... Procrustes: rmse 0.2458423  max resid 0.3462206 
## Run 73 stress 0 
## ... Procrustes: rmse 0.199538  max resid 0.3328155 
## Run 74 stress 5.375749e-07 
## ... Procrustes: rmse 0.1884324  max resid 0.2799996 
## Run 75 stress 0.1275227 
## Run 76 stress 0 
## ... Procrustes: rmse 0.1816124  max resid 0.2437729 
## Run 77 stress 9.811146e-05 
## ... Procrustes: rmse 0.2256537  max resid 0.2778362 
## Run 78 stress 1.100064e-05 
## ... Procrustes: rmse 0.2527877  max resid 0.3396898 
## Run 79 stress 0 
## ... Procrustes: rmse 0.2313656  max resid 0.3294618 
## Run 80 stress 0 
## ... Procrustes: rmse 0.1932941  max resid 0.3496722 
## Run 81 stress 9.89386e-05 
## ... Procrustes: rmse 0.1193919  max resid 0.1825183 
## Run 82 stress 9.932087e-05 
## ... Procrustes: rmse 0.1225201  max resid 0.2318763 
## Run 83 stress 0.0001074903 
## ... Procrustes: rmse 0.1753572  max resid 0.3213585 
## Run 84 stress 0 
## ... Procrustes: rmse 0.1416524  max resid 0.2579267 
## Run 85 stress 0.1275226 
## Run 86 stress 8.237454e-05 
## ... Procrustes: rmse 0.1667862  max resid 0.3144216 
## Run 87 stress 9.826993e-05 
## ... Procrustes: rmse 0.18058  max resid 0.2943438 
## Run 88 stress 9.824521e-05 
## ... Procrustes: rmse 0.1331463  max resid 0.2114605 
## Run 89 stress 0 
## ... Procrustes: rmse 0.2135035  max resid 0.2604271 
## Run 90 stress 1.094076e-05 
## ... Procrustes: rmse 0.2537825  max resid 0.3472056 
## Run 91 stress 8.326869e-06 
## ... Procrustes: rmse 0.2253727  max resid 0.2779884 
## *** No convergence -- monoMDS stopping criteria:
##      1: no. of iterations >= maxit
##     86: stress < smin
##      3: stress ratio > sratmax
##      1: scale factor of the gradient < sfgrmin
## [1] "No Convergence"





  MED Group Representatives Phylogenetic Tree



This tree is a maximum likelihood tree made with the representative sequences from the MED groups formed in the oligotyping analysis using IQTREE2 and the parameters you specified in the vampirus.config file. Also, this is an interactive tree, you can zoom in and hover on nodes to know the sequence ID. For a better visualization of this tree, you can find the *.treefile with bootstrap support values within the results directory and visualize using programs like FigTree or ITOL.